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An historical “wreck”: A transcriptome assembly of the naval shipworm, Teredo navalis Linnaeus, 1978 Mar. Genom. (IF 1.9) Pub Date : 2024-02-27 André Gomes-dos-Santos, Marcos Domingues, Raquel Ruivo, Elza Fonseca, Elsa Froufe, Diana Deyanova, João N. Franco, L. Filipe C. Castro
Historically famous for their negative impact on human-built marine wood structures, mollusc shipworms play a central ecological role in marine ecosystems. Their association with bacterial symbionts, providing cellulolytic and nitrogen-fixing activities, underscores their exceptional wood-eating and wood-boring behaviours, improving energy transfer and the recycling of essential nutrients locked in
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Complete genome sequence analysis of Bacillus velezensis A5, a promising biocontrol agent from the Pacific Ocean Mar. Genom. (IF 1.9) Pub Date : 2024-02-08 Shunhua Ji, Yin Tian, Guangxin Xu, Yiqiang Chen, Jingjing Li, Teng Long, Wei He, Jianqiang Fan, Xixiang Tang
Tobacco bacterial wilt (TBW) caused by is a serious soil-borne disease, which seriously damages the growth of tobacco crops. A5 was isolated from 3000 m deep-sea sediments of the Pacific Ocean, and was found to be antagonistic to TBW. Here, we report the complete genome sequence of strain A5, which has a 4,000,699-bp single circular chromosome with 3827 genes and a G + C content of 46.44%, 87 tRNAs
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Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella) Mar. Genom. (IF 1.9) Pub Date : 2024-02-03 Akifumi Yao, Hisanori Kohtsuka, Toru Miura
The harlequin sandsmelt () is a female-to-male sex change fish in which functional females possess ovotestes that consist of both ovarian and testicular tissues. These features indicate that this species could be an excellent model for studying the flexibility of sex differentiation in vertebrates. However, genetic resources in this species have so far been limited. Therefore, in this study, the reference
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De novo transcriptome sequencing and annotation of the Antarctic polychaete Microspio moorei (Spionidae) with its characterization of the heat stress-related proteins (HSP, SOD & CAT) Mar. Genom. (IF 1.9) Pub Date : 2024-02-01 Idalyd Fonseca-González, Esteban Velasquez-Agudelo, Mario H. Londoño-Mesa, Javier C. Álvarez
We present a transcriptome assembly for the non-model Antarctic polychaete worm (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for The gene sequences of the spionid worm were annotated from a wide range of functions (, biological, and metabolic processes, catalytic processes
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A whole-body transcriptome assembly of the annelid worm Hediste diversicolor Mar. Genom. (IF 1.9) Pub Date : 2024-01-12 André M. Machado, Rodrigo Samico, Marcos Domingues, Andreas Hagemann, Luísa M.P. Valente, Arne M. Malzahn, André Gomes-dos-Santos, Raquel Ruivo, Juan Carlos Navarro, Óscar Monroig, L. Filipe C. Castro
The Annelida phylum is composed of a myriad of species exhibiting key phenotypic adaptations. They occupy key ecological niches in a variety of marine, freshwater and terrestrial ecosystems. Importantly, the increment of resources is rapidly modifying the taxonomic landscape and knowledge of species belonging to this phylum. Here, we comprehensively characterised and annotated a transcriptome of the
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Complete genome sequence of the novel Antarctic Oceanisphaera sp. IT1–181 that carried five plasmids Mar. Genom. (IF 1.9) Pub Date : 2024-01-09 Yong-Qiang Hu, Yi-He Zhang, Wei Han, Ting Hu, Yu Du, Yin-Xin Zeng
Bacteria of the genus in the class are widely distributed in marine environments. sp. IT1–181 was isolated from intertidal sediment in the coastal region of the Chinese Great Wall Station on the Fildes Peninsula, King George Island, Antarctica. Here, we sequenced the complete genome of strain IT1–181, which contained a single chromosome of 3,572,184 bp (G + C content of 49.89 mol%) with five plasmids
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Complete genome sequence of Psychrobacter cibarius AOSW16051, a trimeric autotransporter adhesin synthesizing bacterium isolated from the Baltic Sea Mar. Genom. (IF 1.9) Pub Date : 2023-12-14 Xiao-Yu Wang, Tianyin Miao, Yuyi Wang, Zhangwei Guo, Jin-Long Yang, Xiao Liang
Bacteria of the genus are widely distributed in the global low-temperature marine environment and have been studied for their effects on the settlement and metamorphosis of marine invertebrates. AOSW16051 was isolated from the surface water samples of the Baltic Sea on the edge of the Arctic Ocean. Here, we present the complete genome of strain AOSW16051, which consists of a circular chromosome composed
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Complete genome sequence of carotenoid-producing Aestuariibaculum lutulentum L182T isolated from the tidal sediment Mar. Genom. (IF 1.9) Pub Date : 2023-11-21 Wen-Jia Liu, Jia-Wei Gao, Yu Zhang, Cong Sun, Lin Xu
Aestuariibaculum lutulentum L182T (= KCTC 92530T = MCCC 1K08065T) was isolated from the tidal sediment collected in Beihai, People's Republic of China. The genome was sequenced and consisted of a single chromosome with the size of 3,782,725 bp and DNA G + C content of 35.1%. Genomic annotations demonstrated that it encoded 12 rRNA genes, 56 tRNA genes and 3210 ORFs. The percentages of ORFs assigned
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Complete genome analysis of type strain of a novel bacterial family Temperatibacteraceae fam. nov., isolated from surface seawater Mar. Genom. (IF 1.9) Pub Date : 2023-11-06 Jin-Cheng Rong, Lin-Lin Cui, Xiao-Chen Yang, Mao-Li Yi, Qi Zhao
Novel bacterial resources are valuable for studying bacterial taxonomy, bacterial evolution, and genome mining of novel antibiotics, antitumor agents, and immune modulators. In this study, we de novo sequenced the type strain of a novel bacterial family, Temperatibacteraceae fam. Nov., belonging to class Alphaproteobacteria of phylum Pseudomonadota. The type strain, Temperatibacter marinus NBRC 110045T
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The complete genome sequence of Peribacillus sp. R9–11 for genome mining of polystyrene degrading enzymes Mar. Genom. (IF 1.9) Pub Date : 2023-10-20 Xue Yu, Wenbin Guo, Jingjing Duan
Peribacillus sp. R9–11, isolated from a marine sediment sample of the Arctic Ocean, can grow in mineral medium with polystyrene (PS) plastic as sole carbon source. Here, we present the complete genome of Peribacillus sp. R9–11, which will facilitate the genome mining of PS degrading enzymes. The total length of the sequenced genome consists of 6,288,471 bases, with mean G + C content of 37.93%. A total
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Complete genome sequence of Bacillus cereus Z4, a biocontrol agent against tobacco black shank, isolated from the Western Pacific Ocean Mar. Genom. (IF 1.9) Pub Date : 2023-10-13 Shunhua Ji, Yin Tian, Jingjing Li, Guangxin Xu, Yongan Zhang, Shanyi Chen, Yiqiang Chen, Xixiang Tang
Bacillus species have been considered as promising biological control agents due to their excellent antimicrobial ability. Bacillus cereus strain Z4 was isolated from 2000 m deep sea sediments of the Western Pacific Ocean, which possesses significant antifungal activity against Phytophthora nicotianae, the pathogenic fungus of tobacco black shank disease. To reveal the underlying antifungal genetic
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Genomic analysis of a marine alphaproteobacterium Sagittula sp. strain MA-2 that carried eight plasmids Mar. Genom. (IF 1.9) Pub Date : 2023-09-27 Mayuko Abe, Robert A. Kanaly, Jiro F. Mori
Bacteria that belong to the family Roseobacteraceae in the Alphaproteobacteria class are widely distributed in marine environments with remarkable physiological diversity, which is considered to be attributed to their genomic plasticity. In this study, a novel isolate of the genus Sagittula within Roseobacteraceae, strain MA-2, was obtained from a coastal marine bacterial consortium enriched with aromatic
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Characterization and genomic analysis of a novel Pseudoalteromonas phage PS_L5 Mar. Genom. (IF 1.9) Pub Date : 2023-09-14 Xing Zhou, Jie Gao, Rongda Xiao, Yifan Qiao, Yuang Zhu, Di Zhang, Xinyu Zhang, Huifang Li, Juntian Xu
Pseudoalteromonas is a widely distributed bacterial genus that is associated with marine algae. However, there is still limited knowledge about their bacteriophage. In this study, we reported the isolation of a novel lytic bacteriophage that infects Pseudoalteromonas marina. Transmission electron microscopy revealed that PS_L5 had an icosahedral head of 52.6 ± 2 nm and a non-contractile tail with length
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Complete genome of Polaribacter huanghezhanensis KCTC 32516T isolated from glaciomarine fjord sediment of Svalbard Mar. Genom. (IF 1.9) Pub Date : 2023-08-30 Kyuin Hwang, Hanna Choe, Kyung Mo Kim
Polaribacter huanghezhanensis KCTC 32516T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In
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Size and site specific transcriptomic responses of blue mussel (Mytilus edulis) to acute hypoxia Mar. Genom. (IF 1.9) Pub Date : 2023-08-09 Stephanie Hall, Denise Méthé, Sarah Stewart-Clark, Fraser Clark
The Prince Edward Island (PEI) mussel aquaculture industry is being challenged by climate change induced environmental stressors including hypoxic/anoxic episodes, that can impact mussel health and survival. Physiological responses of mussels to hypoxia/anoxia have been studied; however, less is known about how transcriptomic response leads to physiology. The present study examined the transcriptomic
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Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum Mar. Genom. (IF 1.9) Pub Date : 2023-07-19
One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total
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Complete genome of Rossellomorea sp. DA94, an agarolytic and orange-pigmented bacterium isolated from mangrove sediment of the South China Sea Mar. Genom. (IF 1.9) Pub Date : 2023-07-14
Rossellomorea sp. DA94, isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an agarolytic and orange-pigmented bacterium. Here, we present the complete genome sequence of strain DA94, which comprises 4.63 Mb sequences with 43.5% GC content. In total, 4589 CDSs, 33 rRNA genes and 110 tRNA genes were obtained. Genomic analysis of strain DA94 revealed that 108 CAZymes
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Isolation and genome sequencing of a novel lytic Pseudoalteromonas phage SL20 Mar. Genom. (IF 1.9) Pub Date : 2023-06-28 Huifang Li, Jie Gao, Shiyun Ma, Rongda Xiao, Xing Zhou, Wanting Feng, Siyu Zhao, Jiaqi Luo, Di Zhang
Phage SL20, a novel lytic Pseudoalteromonas phage, was isolated from the coastal waters of the Yellow Sea, China. The microbiological characterization demonstrated that phage SL20 was relatively stable from 35 to 55 °C and the optimal pH was approximately 6.0. A latent period of approximately 24 min was indicated by a one-step growth curve. The burst size was approximately 12 ± 3 PFU/cell. The genome
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Complete genome sequence of pectin-degrading Flavobacteriaceae bacterium GSB9 Mar. Genom. (IF 1.9) Pub Date : 2023-06-28 Binna Lee, Jeong Ah. Kim, Yunjon Han, Jae Jun Song, Jong Hyun Choi, Ji Young Kang
Pectic oligosaccharides, which are considered to be potential prebiotics, may be generated by pectin-degrading enzymes. Here, we report the complete genome sequence of the pectin-degrading marine bacterium, Flavobacteriaceae bacterium GSB9, which was isolated from seawater of South Korea. The complete genome sequence revealed that the chromosome was 3,630,376 bp in size, had a G + C content of 36.6 mol%
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Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent Mar. Genom. (IF 1.9) Pub Date : 2023-06-21 Xue-Gong Li, Jie Dai, Wei-Jia Zhang, Ai-Jun Jiang, Deng-Hui Li, Long-Fei Wu
Tepidibacter sp. SWIR-1, a putative new species isolated from deep-sea hydrothermal vent field on the Southwest Indian Ridge (SWIR), is an anaerobic, mesophilic and endospore-forming bacterium belonging to the family Peptostreptococcaceae. In this study, we present the complete genome sequence of strain SWIR-1, consists of a single circular chromosome comprising 4,122,966 nucleotides with 29.25% G + C
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Complete genome sequence of Halomonas alkaliantarctica MSP3 isolated from marine sediment, Jeju Island Mar. Genom. (IF 1.9) Pub Date : 2023-06-08 Minji Kim, Soo-Je Park
As a moderate halophilic-heterotrophic bacterium, Halomonas alkaliantarctica MSP3 was isolated from marine sediment located in Jeju island, South Korea. The complete genome of strain MSP3 was sequenced and analyzed to reveal its genetic features and metabolic potential. The genome size of MSP3 was about 4.23 Mbp with 54.7% G + C content, and it contained 3811 protein-coding sequences and 79 RNA genes
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Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean Mar. Genom. (IF 1.9) Pub Date : 2023-05-26 Xiao-Lan Yue, Lin Xu, Li Cui, Ge-Yi Fu, Xue-Wei Xu
Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern
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A first annotated genome sequence for Haliotis midae with genomic insights into abalone evolution and traits of economic importance Mar. Genom. (IF 1.9) Pub Date : 2023-05-15 Thendo S. Tshilate, Edson Ishengoma, Clint Rhode
Haliotis midae or “perlemoen” is one of five abalone species endemic to South Africa, and being palatable, the only commercially important abalone species with a high international demand. The higher demand for this abalone species has resulted in the decrease of natural stocks due to overexploitation by capture fisheries and poaching. Facilitating aquaculture production of H. midae should assist in
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Genomic analysis of Marinomonas algicola SM1966T reveals its role in marine sulfur cycling Mar. Genom. (IF 1.9) Pub Date : 2023-04-30 Min Zhang, Xiao-Di Wang, Yue Lin, Shu-Yan Wang, Shan Zhang, Jin Cheng, Mei-Ling Sun, Peng Wang, Hui-Hui Fu, Chun-Yang Li, Nan Zhang
Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling, which is mainly produced by marine phytoplankton and macroalgae. Marinomonas algicola SM1966T, a Gram-negative, aerobic and rod-shaped bacterium, was isolated from the surface of Ulva pertusa (Chlorophyta) algal sample collected off the coastal areas
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Complete genome sequence of Streptomyces sp. HNA39, a new cyclizidine producer isolated from a South China Sea sediment Mar. Genom. (IF 1.9) Pub Date : 2023-04-27 Suzhen Li, Yong-Jun Jiang, Zhongjun Ma, Nan Wang
Streptomyces sp. HNA39 is a promising candidate for the production of antineoplastic metabolites screened from a collection of 448 actinomycetes derived from coastal sediments. The complete genome sequence of HNA39 comprises a 7,351,753-bp linear chromosome with a GC content of 71.94%. Whole genome analysis reveals the presence of 29 putative biosynthetic gene clusters (BGCs) encoding secondary metabolites
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Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community Mar. Genom. (IF 1.9) Pub Date : 2023-04-19 Manar El Samak, Samira Zakeer, Amro Hanora, Samar M. Solyman
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Genomic insights into secondary metabolites of pharmaceutical utility for Hyphococcus flavus MCCC 1K03223T, isolated from bathypelagic seawater Mar. Genom. (IF 1.9) Pub Date : 2023-04-14 Jin-Cheng Rong, Li Sheng, Li-Hua Jiang, Mao-Li Yi, Jin-Ying Wu, Qi Zhao
During an attempt to screen secondary metabolites of pharmaceutical utility, we sequenced the complete genome of type strain of a novel marine bacterial genus, named genus Hyphococcus. The type strain, Hyphococcus flavus MCCC 1K03223T, was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223T is composed of a circular chromosome of
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Shotgun metagenomic analysis of bacterial symbionts associated with “Chromodoris quadricolor” mantle Mar. Genom. (IF 1.9) Pub Date : 2023-04-11 Engy Mahmoud, Amro Hanora, Salah Abdalla, Ali A. Abdelrahman Ahmed, Samira Zakeer
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Complete genome sequence of Bacillus cereus 2-6A, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Pacific Ocean Mar. Genom. (IF 1.9) Pub Date : 2023-04-03 Xuan Zou, Chuan-Lei Suo, Xiao-Mei Geng, Chun-Yang Li, Hui-Hui Fu, Yi Zhang, Peng Wang, Mei-Ling Sun
Bacillus cereus 2-6A, was isolated from the sediments in the hydrothermal area of the Pacific Ocean with a water depth of 2628 m. In this study, we report the whole genome sequence of strain 2-6A and analyze that to understand its metabolic capacities and biosynthesis potential of natural products. The genome of strain 2-6A consists of a circular chromosome of 5,191,018 bp with a GC content of 35.3 mol%
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Complete genome sequence of Pseudoalteromonas sp. PS1M3, a psychrotrophic bacterium isolated from deep-sea sediment off the Boso Peninsula, Japan Trench Mar. Genom. (IF 1.9) Pub Date : 2023-03-28 Yoshihito Nikaidou, Yong Guo, Mahoko Taguchi, Shigeru Chohnan, Tomoyasu Nishizawa, Yasurou Kurusu
Herein, we report the complete genome sequence of Pseudoalteromonas sp. PS1M3 (= NCBI 87791), which is a psychrotrophic bacterium that inhabits in seabed off the Boso Peninsula, Japan Trench. Analysis of the genomic sequence revealed that PS1M3 possesses 2 circular chromosomal DNAs and 2 circular plasmid DNAs. The genome of PS1M3 had a total size of 4,351,630 bp, an average GC content of 39.9%, and
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ROS-dependent cell death of Heterosigma akashiwo induced by algicidal bacterium Hahella sp. KA22 Mar. Genom. (IF 1.9) Pub Date : 2023-03-13 Qun Lin, Jiarong Feng, Zhong Hu, Runlin Cai, Hui Wang
Marine algicidal bacteria and their metabolites are considered to be one of the most effective strategies to mitigate the harmful algal blooms (HABs). The bacterium Hahella sp. KA22 has previously been confirmed to have strong algicidal activity against the HABs causing microalgae, Heterosigma akashiwo. In this study, the molecular mechanism of microalgae cell death was detected. The results showed
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Complete genome of Mycolicibacterium phocaicum RL-HY01, a PAEs-degrading marine bacterial strain isolated from Zhanjiang Bay, China Mar. Genom. (IF 1.9) Pub Date : 2023-03-02 Yuduan Ou, John L. Zhou, Yang Jia, Mei Liang, Hanqiao Hu, Lei Ren
Mycolicibacterium phocaicum RL-HY01, a marine bacterial strain with the capability to degrade phthalic acid esters (PAEs), was isolated from Zhanjiang Bay, China. Here, the complete genome sequence of strain RL-HY01 was presented. The genome of strain RL-HY01 contains one circular chromosome of 6,064,759 bp with a G + C content of 66.93 mol%. The genome contains 5681 predicted protein-encoding genes
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Complete genome analysis of Bacillus subtilis TY-1 reveals its biocontrol potential against tobacco bacterial wilt Mar. Genom. (IF 1.9) Pub Date : 2023-02-24 Yin Tian, Shunhua Ji, Enren Zhang, Yiqiang Chen, Guangxin Xu, Xi Chen, Jianqiang Fan, Xixiang Tang
Bacillus subtilis TY-1 was isolated from 2000 m-deep sea sediments of the Western Pacific Ocean, which was found to exhibit strong antagonistic activity against tobacco bacterial wilt caused by Ralstonia solanacearum. Here, we present the annotated complete genomic sequence of the strain Bacillus subtilis TY-1. The genome consists of a 4,030,869-bp circular chromosome with a G + C content of 43.88%
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Mining Chromodoris quadricolor symbionts for biosynthesis of novel secondary metabolites Mar. Genom. (IF 1.9) Pub Date : 2023-02-02
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Complete genome sequence of one novel marine Pseudomonas sp. BSw22131 growing with dimethylsulfoniopropionate (DMSP) as the sole carbon source Mar. Genom. (IF 1.9) Pub Date : 2023-01-23 Ting Hu, Yin-Xin Zeng, Yi-He Zhang, Yu Du, Wei Han, Hui-Rong Li, Wei Luo
Members of the genus Pseudomonas have been frequently isolated from the marine environment, indicating their ecological role in native habitats. One bacterial strain, Pseudomonas sp. BSw22131, was isolated from seawater in Kongsfjorden, Svalbard. The bacterium can grow with algae-derived dimethylsulfoniopropionate (DMSP) as the sole carbon source. Here, we sequenced the complete genome of strain BSw22131
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Bioactivity of bacteria associated with Red Sea nudibranchs and whole genome sequence of Nocardiopsis dassonvillei RACA-4 Mar. Genom. (IF 1.9) Pub Date : 2022-12-13 Hossam H. Elfeky, Amro Hanora, Samar M. Solyman
Microorganisms associated with marine invertebrates consider an important source of bioactive products. This study aimed to screen for antimicrobial and anticancer activity of crude extracts of bacteria associated with Red sea nudibranchs and molecular identification of the bioactive isolates using 16Sr RNA sequencing, in addition to whole-genome sequencing of one of the most bioactive bacteria. This
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Genomic analysis of Marinimicrobium sp. C6131 reveals its genetic potential involved in chitin metabolism Mar. Genom. (IF 1.9) Pub Date : 2022-12-14 Yan-Ru Dang, Xiao-Yu Zhang, Sha-Sha Liu, Ping-Yi Li, Xue-Bing Ren, Qi-Long Qin
Marinimicrobium sp. C6131, which had the ability to degrade chitin, was isolated from deep-sea sediment of the southwest Indian Ocean. Here, the genome of strain C6131 was sequenced and the chitin metabolic pathways were constructed. The genome contained a circular chromosome of 4,207,651 bp with a G + C content of 58.50%. A total of 3471 protein-coding sequences were predicted. Gene annotation and
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The complete genome sequence of Pseudomonas chengduensis BC1815 for genome mining of PET degrading enzymes Mar. Genom. (IF 1.9) Pub Date : 2022-12-14 Zhengguang Shi, Xue Yu, Jingjing Duan, Wenbin Guo
Pseudomonas chengduensis BC1815, isolated from a marine sediment sample of the Pacific Ocean, can grow in mineral medium with PET plastic as sole carbon source. Here, we present the complete genome of Pseudomonas chengduensis BC1815, which will facilitate the genome mining of PET degrading enzymes. The total length of the sequenced genome consists of 5,578,440 bases, with mean G + C content of 62.65%
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De novo transcriptomes for two species of snappers from the Western Atlantic (Lutjanus griseus and Lutjanus synagris) Mar. Genom. (IF 1.9) Pub Date : 2022-11-23 Adam Hallaj, Logan F. Turner, Carolyn A. McArdle, Moisés A. Bernal
Transcriptomes are appropriate resources for studying species that lack sequenced genomes, as they can serve as references for a broad suite of genetic applications, including: phylogenetic assessments, population genomics, and evaluate responses to environmental fluctuations. Here, we present the transcriptomes of two species of marine fishes of commercial and ecological relevance in the Western Atlantic:
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Transcriptome assemblies of two deep-sea octocorals Calyptrophora lyra and Chrysogorgia stellata from West Pacific seamount, Godin Guyot Mar. Genom. (IF 1.9) Pub Date : 2022-11-22 Taewoo Ryu, Sung-Jin Hwang, Seonock Woo
This is the first report of the transcriptome assemblies of the deep-sea octocorals Calyptrophora lyra and Chrysogorgia stellata, which were collected in a survey of the West Pacific seamounts area. We sequenced the transcriptomes of C. lyra and C. stellata using the Illumina NovaSeq 6000 System. De novo assembly and analysis of the coding regions predicted 193,796 unigenes from the total 116,441,796
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Complete genome sequence of marine Roseobacter lineage member Ruegeria sp. YS9 with five plasmids isolated from red algae Mar. Genom. (IF 1.9) Pub Date : 2022-11-11 Qun-Jian Yin, Fang-Chao Zhu, Hong-Zhi Tang, Xu-Yang Chen, Xin Liu, Li-Chang Tang, Xue-Gong Li
Ruegeria sp. YS9, an aerobic and chemoheterotrophic bacterium belonging to marine Roseobacter lineage, was a putative new species isolated from red algae Eucheuma okamurai in the South China Sea (Beihai, Guangxi province). The complete genome sequence in strain YS9 comprised one circular chromosome with 3,244,635 bp and five circular plasmids ranging from 38,085 to 748,160 bp, with a total length of
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Complete genome sequence of piezotolerant Stutzerimonas kunmingensis 7850S isolated from the sediment of the Mariana Trench Mar. Genom. (IF 1.9) Pub Date : 2022-11-08 Jia-Wei Wang, Kun Shang, Sheng-Yi Wu, Bo-Yu Zhu, Mei-Gui Han, Yuan Zhao, Yi-Qiu Chen, Jia Xie, Bo Huang, Zhuang Han
Stutzerimonas kunmingensis 7850S is a piezotolerant bacterium isolated from the sediment of the Mariana trench. Here, we described the complete genome of strain 7850S, which contains a single circular chromosome of 4,775,870 base pairs with 62.66% G + C content, and harbors 4494 protein-coding genes, 65 transfer RNA genes, and 12 ribosomal RNA genes. The experimental results showed that strain 7850S
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Complete genome sequence of the denitrifying Pseudomonas sp. strain DNDY-54 isolated from deep-sea sediment of ninety east ridge Mar. Genom. (IF 1.9) Pub Date : 2022-10-23 Luying Zhao, Yuanyuan Gui, Ao Zhang, Qian Zhang, Liping Fu, Jiang Li
Pseudomonas sp. strain DNDY-54, a denitrifying bacterium, was isolated from a deep-sea sediment sample from Ninety East Ridge in the Indian Ocean. Here, we show that the complete genome of DNDY-54 has one circular chromosome of 4,412,895 bp with mean 60.57% GC content. The complete genome contains 4111 predicted protein-coding genes, 59 tRNAs, and 4 rRNA operons as 16S–23S-5S rRNA. On the basis of
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Bacterial diversity associated with the excavating sponge Thoosa mismalolli from East Pacific Coral reefs Mar. Genom. (IF 1.9) Pub Date : 2022-10-18 Adrián González-Castillo, José Luis Carballo, Eric Bautista-Guerrero
Thoosa mismalolli is one of the most abundant and common excavating sponges along Mexican and Central America shallow reefs. This sponge harbors a microbiome unknown so far. In the present study, the metagenome of T. mismalolli was sequenced, and total reads obtained were classified, and contigs were assembled to analyze the microbiota. The results showed that the highest number of contigs was assigned
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De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress Mar. Genom. (IF 1.9) Pub Date : 2022-09-15 Andrew Ndhlovu, Sophie von der Heyden
Seagrasses are important marine ecosystem engineers but anthropogenic impacts and climate change have led to numerous population declines globally. In South Africa, Zostera capensis is endangered due to fragmented populations and heavy anthropogenic pressures on estuarine ecosystems that house the core of the populations. Addressing questions of how pressures such as climate change affect foundational
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Bimodal distribution of seafloor microbiota diversity and function are associated with marine aquaculture Mar. Genom. (IF 1.9) Pub Date : 2022-09-15 R. Pettersen, I. Ormaasen, I.L. Angell, N.B. Keeley, A. Lindseth, L. Snipen, K. Rudi
The aim of the current work was to investigate the impact of marine aquaculture on seafloor biogeochemistry and diversity from pristine environments in the northern part of Norway. Our analytical approach included analyses of 182 samples from 16 aquaculture sites using 16S and 18S rRNA, shotgun analyses, visual examination of macro-organisms, in addition to chemical measurements. We observed a clear
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Complete genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of Gilvimarinus sp. DA14 isolated from the South China Sea Mar. Genom. (IF 1.9) Pub Date : 2022-08-27 Qun-Jian Yin, Hong-Zhi Tang, Fang-Chao Zhu, Xu-Yang Chen, De-Wei Cheng, Li-Chang Tang, Xiao-Qing Qi, Xue-Gong Li
Gilvimarinus sp. DA14, a putative new species isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an aerobic and heterotrophic agar degrading bacterium. Here, we present the complete genome sequence of strain DA14, which comprises 3.96 Mb sequences with 53.39% GC content. In total, 3391 CDSs, 6 rRNA genes and 44 tRNA genes were obtained. Genomic analysis of strain
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Transcriptome responses in copepods Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus exposed to phenanthrene and benzo[a]pyrene Mar. Genom. (IF 1.9) Pub Date : 2022-08-12 Fekadu Yadetie, Nadja R. Brun, Julia Giebichenstein, Katarzyna Dmoch, Ketil Hylland, Katrine Borgå, Odd André Karlsen, Anders Goksøyr
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Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition Mar. Genom. (IF 1.9) Pub Date : 2022-08-10 Zoya Harbuzov, Valeria Farberova, Moshe Tom, Alberto Pallavicini, David Stanković, Tamar Lotan, Hadas Lubinevsky
The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470–490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using
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Complete genome sequencing and analysis revealed the nitrogen utilization strategy of a novel Acuticoccus species isolated from surface water of the Indian Ocean Mar. Genom. (IF 1.9) Pub Date : 2022-07-19 Jie Shi, Yufeng Zeng, Huan Wang, Yuanyuan Niu, Peiqing He, Hao Chen
Acuticoccus sp. I52.16.1 was isolated from 100 m water depth from the Indian Ocean, and presented a novel Acuticoccus species belonging to the family Acuticoccaceae, class Alphaproteobacteria. The strain I52.16.1 displayed the activities of nitrate reductase, nitrite reductase, and urease. The genome of Acuticoccus sp. I52.16.1 consisted of a circular chromosome (5, 134, 086 bp) with a G + C content
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Transcriptome profiling of the early developmental stages in the giant mussel Choromytilus chorus exposed to delousing drugs Mar. Genom. (IF 1.9) Pub Date : 2022-07-12 Gustavo Núñez-Acuña, Camila Fernandez, Sandra Sanhueza-Guevara, Cristian Gallardo-Escárate
The giant mussel Choromytilus chorus is a marine bivalve commonly collected in central – southern Chile from fishery zones shared with the salmon industry. These economically relevant areas are also affected by the use of pesticides for controlling sea lice infestations in salmon aquaculture. Their main target is the sea louse Caligus rogercresseyi. However, other than some physiological impacts, the
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Aquaculture omics: An update on the current status of research and data analysis Mar. Genom. (IF 1.9) Pub Date : 2022-06-29 Jitendra Kumar Sundaray, Sangita Dixit, Ashraf Rather, Kiran D. Rasal, Lakshman Sahoo
Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional
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Complete genome sequence of Devosia beringensis S02T, a type strain with genes involved in deoxynivalenol degradation Mar. Genom. (IF 1.9) Pub Date : 2022-06-28 Pu-Yu Hao, Hui-Rong Li, Wei Luo, Ren Xu, Yin-Xin Zeng
Members of the genus Devosia are known for their abilities to degrade deoxynivalenol (DON). The type strain Devosia beringensis S02T (= JCM 33772 = CCTCC AB 2019343) was isolated from sediment of the Bering Sea and identified in 2021. However, the genome sequence of D. beringensis S02T remains unclear, which complicates the exploration into the function and ecological role of this strain in marine
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Transcriptome analysis of the ink sac and brain tissues from Sepiella inermis: A resource for discovering genes related to the inking of cephalopods Mar. Genom. (IF 1.9) Pub Date : 2022-06-27 Shanshan Zhou, Tao Zhang, Cuili Wang, Jun Liang, Pengfei Li, Kaida Xu, Hengtong Qiu
The common Chinese cuttlefish (Sepiella inermis) is an important cephalopod with nutritional and commercial value. Intensive inking stimulated by swilling seawater in transfer containers threatens the survival of cephalopods during transportation. However, the molecular basis for the inking behavior of S. inermis remains unclear. In the present study, transcriptome analysis was performed on ink sac
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Genomic analysis of Shewanella eurypsychrophilus YLB-09 reveals backgrounds related to its deep sea environment adaptation Mar. Genom. (IF 1.9) Pub Date : 2022-05-19 Xiaorong Cao, Zhiwei Yi, Xu Qiu, Huangming Wu, Libo Yu, Xixiang Tang
Shewanella eurypsychrophilus YLB-09 is a psychrophilic and piezotolerant bacterium that was isolated from 2699 m deep sea sediments of the Southwest Indian Ocean. The complete genome sequence of the strain Shewanella eurypsychrophilus YLB-09 was analyzed. The genome of Shewanella eurypsychrophilus YLB-09 contained one single circular chromosome 6,225,487 base pairs with a 43.6 mol% G + C content of